CBI Molecules

These are molecules under study by members of the University of Massachusetts Amherst Chemistry-Biology Interface Program. Many of the molecules we study are featured at the Molecular Playground (see also Molecular Playground in Proteopedia). Follow the links below to read nontechnical descriptions, in Proteopedia, of the molecules displayed in Molecular Playground.

UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.

It's great to build on a previous entry, but you must leave the earlier one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.

Fall 2010: New entries are due 12/10/10. Please append the designation (new Fall 2010) to your new entries.

Spring 2011: New entries are due 5/4/11. Please append the designation (new Spring 2011) to your new entries

Bhatia Lab
 * Molecular Playground/Alginate, David Griffin


 * Molecular Playground/Alginate-Fall2010, Joe White, David Griffin (new Fall 2010)


 * Molecular Playground/Poly(ethylene glycol), Erika M. Saffer (new Spring 2011)

Chambers Lab


 * Molecular Playground/Glutamate Receptor, Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano

Chien Lab


 * Molecular Playground/Hexameric ClpX, Joanne Lau (new Fall 2010)

Forbes Lab


 * Molecular Playground/TRAIL, Charley Swofford


 * Molecular Playground/CheR, Miaomin Zhang (new Spring 2011)


 * Molecular Playground/RBP, Jan Panteli (new Spring 2011)

Garman Lab


 * Molecular Playground/Human Protective Protein Cathepsin A, Yadilette Rivera-Colon


 * Molecular Playground/Human PPCA, Nilima Kolli

Gierasch Lab


 * Molecular Playground/CRABP I, Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy
 * Best Overall CBI Molecule 2010

Hardy Lab


 * Molecular Playground/Caspase-7 Dynamics


 * Molecular Playground/Caspase-9 Regulation, Kristen Huber


 * Molecular Playground/Caspase-6 (new), Elih Velazquez


 * Molecular Playground/Influenza A M2 transmembrane domain, Samantha Nicholls


 * Molecular Playground/Dengue Virus Protease, Muslum Yildiz

Hebert Lab


 * Molecular_Playground/ERMan1, Johan Sunryd


 * Molecular Playground/Saposin C, Abla Tannous (New Spring 2011)

Heuck Lab


 * Molecular_Playground/Pcr H, Fabian Romano (New Fall 2010)

Kaltashov Lab


 * Molecular Playground/Velaglucerase, Adriana Kita

Knapp lab
 * Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme, Cristina Martin
 * Best CBI Molecule Proteopedia Page 2010


 * Molecular Playground/FIH, Cornelius Taabazuing, Breanne Holmes, John Hangasky

Martin Lab


 * Molecular Playground/T7 RNA Polymerase (7 mer int), Ankit Vahia
 * Molecular Playground/T7 RNAP Conformations, Luis E. Ramirez-Tapia (New Spring 2011)

Roberts Lab


 * Molecular Playground/Taxol, Rohan Patil, Sarah Wilson


 * Molecular Playground/Insulin, Whitney Stoppel

Rotello Lab


 * Molecular Playground/Reverse Transcriptase, Daniel Moyano-Marino


 * Molecular Playground/Pancreatic Lipase, Rui Tang


 * Molecular playground/Chymotrypsin, Brad


 * Molecular Playground/Targeting Peptide, David Solfiell

Schnarr Lab


 * Molecular Playground/6-Deoxyerythronolide B Synthase, Tsung-Yi Lin, Jon Amoroso


 * Molecular Playground/ACP apo, Gitanjeli Prasad

Thayumanavan Lab


 * Molecular Playground/Lysozime , Daniella Gonzalez


 * Molecular Playground/Beta-galactosidase, Judy Ventura


 * Molecular Playground/Carbonic Anhydrase, Krishna Reddy Raghupathi


 * Molecular Playground/Avidin, Rami Rajasekar Reddy


 * Molecular Playground/Biotin binding avidin, Diego Amado


 * Molecular Playground/MMP12, Jiaming Zhuang


 *  Molecular Playground/Gluconase, Jing Guo


 * Molecular Playground/Glutathione Reductase, Reuben Chacko

Thayumanavan & Vachet Labs


 * Molecular Playground/Trypsin, Gladys Murage

Thompson & Weis Labs


 * Molecular Playground/Bacterial Chemotaxis Receptors, Lynmarie K. Thompson, Shiela M. Jones


 * Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor, Meili Yang

Vachet Lab


 * Molecular playground/beta 2 microglobulin, Nick Borotto
 * Best CBI Molecule Jmol scenes 2010


 * Molecular Playground/Myoglobin, Yuping Zhou


 * Molecular Playground/ Copper-Zinc Superoxide Dismutase, Shaynah Browne (NEW FALL 2010)

Other Molecules of interest


 * Molecular Playground/PcrA Helicase, Luis E Ramirez-Tapia, Martin Lab

Other Laboratories


 * Molecular Playground/YKL-40, Ralph A. Francescone III, Shao Lab


 * Molecular Playground/β-lactoglobulin, Daniel Seeman, Dubin Lab


 * Molecular Playground/ADAM13, Genevieve Abbruzzese, Alfandari Lab

Instructions:

'''Congratulations to the prize-winning CBI molecules noted above! These also provide great examples to follow. Another prize for best CBI Molecules page and/or scene will be awarded in spring 2011!'''

Choose a molecule that is part of your research project.

1. If you don't already have one, request a Proteopedia account and log in. If you are new to Proteopedia, click Help in the navigation box on the left to get started.

2. Make yourself a sandbox page in which you will develop your CBI Molecule scene and description (Enter "User:your name/sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. See example User:Lynmarie K Thompson/Sandbox 1).

3. Follow the format of the sample CBI molecule page Molecular Playground/Bacterial Chemotaxis Receptors. Easiest way to do this is to copy this page (in editing mode), paste it into your sandbox page, keep the first paragraph about CBI molecules, and then edit to describe and display your molecule. Your goal is to make this an interesting, nontechnical description of the molecule. If multiple people in one group work on the same molecule, you can each make different scenes for the same CBI molecule and each describe them on the same proteopedia page. Talk with each other about your plans so you are not duplicating efforts.

4. Create an attractive scene for your molecule: use the scene authoring tools in the edit mode to create the view you like, then copy the wiki text into your window.

5. Choose a "green scene" on your Proteopedia page to suggest for display at the Molecular Playground and specify a "banner" which will be projected with the molecule. This should be a short, one-line headline for your scene that includes the name of the molecule and what is important about the scene or the molecule. Remember to design this for the general public, including non-scientists. My example is: "Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment."

6. When you are happy with your sandbox page, make yourself a permanent Proteopedia page, which will be editable by others. Enter "Molecular Playground/your molecule" (omit quotes) in the search box, then follow the instructions to create a new page with this title. Copy the content of your sandbox to this new page.

7. When you have finished the final version of your page and scene, edit this CBI Molecules page to add a listing and link for your molecule, following the "Bacterial chemotaxis receptors" example above. Please list your lab group, with your name in parentheses. That way more than one name can be associated with a Molecular Playground page (if there are several students on the Molecular Playground page, please indicate your scene with your initials). It would be great to link the lab names to web pages too.